scholarly journals Ignatzschineria indica sp. nov. and Ignatzschineria ureiclastica sp. nov., isolated from adult flesh flies (Diptera: Sarcophagidae)

2011 ◽  
Vol 61 (6) ◽  
pp. 1360-1369 ◽  
Author(s):  
Arvind Kumar Gupta ◽  
Mahesh Shantappa Dharne ◽  
Ashraf Yusuf Rangrez ◽  
Pankaj Verma ◽  
Hemant V. Ghate ◽  
...  
Keyword(s):  
16S Rrna ◽  
Dna Hybridization ◽  
Type Strain ◽  
Gene Sequence ◽  
Sequence Data ◽  
Sequence Similarity ◽  
23S Rrna ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Flesh Flies

Two Gram-negative-staining, aerobic, non-motile, rod-shaped bacteria, designated strains FFA1T and FFA3T, and belonging to the class Gammaproteobacteria were isolated from the gastrointestinal tract of adult flesh flies (Diptera: Sarcophagidae). Phylogenetic analysis of 16S rRNA gene sequence data placed these two strains within the genus Ignatzschineria with similarities of 98.6 % (FFA1T) and 99.35 % (FFA3T) to Ignatzschineria larvae L1/68T. The level of gene sequence similarity between strains FFA1T and FFA3T was 99 %, 97.15 % and 78.1 % based on the 16S rRNA, 23S rRNA and gyrB gene sequences, respectively. Strains FFA1T and FFA3T shared 24 % DNA–DNA relatedness. DNA–DNA hybridization revealed a very low level of relatedness between the novel strains (22 % for strain FFA1T and 44 % for strain FFA3T) and I. larvae L1/68T genomic DNA. The respiratory quinone was Q-8 in both novel strains. The DNA G+C contents were 41.1 mol% and 40.1 mol% for strains FFA1T and FFA3T, respectively. The cell membrane of both strains consisted of phosphatidylglycerol, phosphatidylethanolamine, phospholipids and aminophospholipid. The major fatty acids for both strains were C16 : 0, summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), CyC19 : 0ω8c and C14 : 0. The results of DNA–DNA hybridization between the two new strains and I. larvae L1/68T, in combination with phylogenetic, chemotaxonomic, biochemical and electron microscopic data, demonstrated that strains FFA1T and FFA3T represented two novel species of the genus Ignatzschineria for which the names Ignatzschineria indica sp. nov. (type strain FFA1T = DSM 22309T = KCTC 22643T = NCIM 5325T) and Ignatzschineria ureiclastica sp. nov. (type strain FFA3T = DSM 22310T = KCTC 22644T = NCIM 5326T) are proposed.

scholarly journals Effusibacillus dendaii sp. nov. isolated from farm soil

2021 ◽  
Author(s):  
Tomoyuki Konishi ◽  
Tomohiko Tamura ◽  
Toru Tobita ◽  
Saori Sakai ◽  
Namio Matsuda ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Respiratory Quinone ◽  
Genome Analyses

Abstract Gram-positive, rod-shaped, spore-forming, thermophilic, acidophilic bacterium, designated strain skT53T, was isolated from farm soil in Tokyo, Japan. The strain grew aerobically at 37–55°C (optimum 50°C) and pH 4.0–6.0 (optimum 5.0). Phylogenetic analysis of the 16S rRNA gene sequence showed that the isolate was most closely related to the type strain of Effusibacillus consociatus (94.3% similarity). The G + C content of the genomic DNA was 48.22 mol%. MK-7 was the predominant respiratory quinone. The major fatty acids were anteiso-C15:0, iso-C15:0, iso-C16:0 and C18:3ω6c. The results of phenotypic and chemotaxonomic, 16S rRNA gene sequence similarity, and whole genome analyses support strain skT53T as representing a novel species of Effusibacillus dendaii sp. nov. is proposed. The type strain is strain skT53T (= NBRC 114101T = TBRC 11241T).

scholarly journals Gracilibacillus ureilyticus sp. nov., a halotolerant bacterium from a saline–alkaline soil

2010 ◽  
Vol 60 (6) ◽  
pp. 1383-1386 ◽  
Author(s):  
Ying-Yi Huo ◽  
Xue-Wei Xu ◽  
Heng-Lin Cui ◽  
Min Wu
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Alkaline Soil ◽  
Rrna Gene Sequence ◽  
Respiratory Quinone

A Gram-stain-positive, halotolerant, neutrophilic, rod-shaped bacterium, strain MF38T, was isolated from a saline–alkaline soil in China and subjected to a polyphasic taxonomic characterization. The isolate grew in the presence of 0–15 % (w/v) NaCl and at pH 6.5–8.5; optimum growth was observed with 3.0 % (w/v) NaCl and at pH 7.0. Chemotaxonomic analysis showed menaquinone MK-7 as the predominant respiratory quinone and anteiso-C15 : 0, anteiso-C17 : 0, iso-C15 : 0, C17 : 0 and C16 : 0 as major fatty acids. The genomic DNA G+C content was 35.3 mol%. 16S rRNA gene sequence similarities of strain MF38T with type strains of described Gracilibacillus species ranged from 95.3 to 97.7 %. Strain MF38T exhibited the closest phylogenetic affinity to the type strain of Gracilibacillus dipsosauri, with 97.7 % 16S rRNA gene sequence similarity. The DNA–DNA reassociation between strain MF38T and G. dipsosauri DSM 11125T was 45 %. On the basis of phenotypic and genotypic data, strain MF38T represents a novel species of the genus Gracilibacillus, for which the name Gracilibacillus ureilyticus sp. nov. (type strain MF38T =CGMCC 1.7727T =JCM 15711T) is proposed.

scholarly journals Vibrio variabilis sp. nov. and Vibrio maritimus sp. nov., isolated from Palythoa caribaeorum

2011 ◽  
Vol 61 (12) ◽  
pp. 3009-3015 ◽  
Author(s):  
Luciane A. Chimetto ◽  
Ilse Cleenwerck ◽  
Ana Paula B. Moreira ◽  
Marcelo Brocchi ◽  
Anne Willems ◽  
...  
Keyword(s):  
16S Rrna ◽  
Dna Hybridization ◽  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Phenotypic Characterization ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Palythoa Caribaeorum ◽  
Separate Branch

Two novel vibrio isolates (R-40492T and R-40493T) originating from the zoanthid Palythoa caribaeorum in Brazil in 2005 were taxonomically characterized by means of a polyphasic approach comprising multilocus sequence analysis (MLSA), DNA–DNA hybridization (DDH), ΔT m analysis and phenotypic characterization. Phylogenetic analysis based on 16S rRNA gene sequences showed that R-40492T and R-40493T fell within the genus Vibrio and were most closely related to each other with 99 % similarity; similarities of these two novel isolates towards Vibrio neptunius LMG 20536T, Vibrio coralliilyticus LMG 20984T, Vibrio nigripulchritudo LMG 3896T, Vibrio sinaloensis LMG 25238T and Vibrio brasiliensis LMG 20546T varied between 97.1 and 98.5 %. DDH experiments showed that the two isolates had less than 15 % relatedness to the phylogenetically most closely related Vibrio species. R-40492T and R-40493T had 55–57 % relatedness to each other. The ΔTm between R-40492T and R-40493T was 6.12 °C. In addition, MLSA of concatenated sequences (16S rRNA, ftsZ, gyrB, recA, rpoA, topA, pyrH and mreB; 6035 bp in length) showed that the two novel isolates formed a separate branch with less than 92 % concatenated gene sequence similarity towards known species of vibrios. Two novel species are proposed to accommodate these novel isolates, namely Vibrio variabilis sp. nov. (type strain, R-40492T = LMG 25438T = CAIM 1454T) and Vibrio maritimus sp. nov. (type strain, R-40493T = LMG 25439T = CAIM 1455T).

scholarly journals Effusibacillus dendaii sp. nov. isolated from farm soil

2021 ◽  
Author(s):  
Tomoyuki Konishi ◽  
Tomohiko Tamura ◽  
Toru Tobita ◽  
Saori Sakai ◽  
Namio Matsuda ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Respiratory Quinone ◽  
Genome Analyses

AbstractA Gram-positive, rod-shaped, spore-forming, thermophilic, and acidophilic bacterium, designated as strain skT53T, was isolated from farm soil in Tokyo, Japan. Under aerobic conditions, the strain grew at 35–55 °C (optimum temperature 44–55 °C) and pH 4.0–6.0 (optimum pH 5.0). Phylogenetic analysis of the 16S rRNA gene sequence showed that the isolate was moderately related to the type strain of Effusibacillus consociatus (94.3% similarity). The G + C content of the genomic DNA was 48.2 mol%, and MK-7 was the predominant respiratory quinone in the strain. The major fatty acids were anteiso-C15:0, iso-C15:0, and iso-C16:0. Based on the phenotypic and chemotaxonomic characteristics, as well as 16S rRNA gene sequence similarity and whole genome analyses, strain skT53T represents a novel species in the genus Effusibacillus, for which the name Effusibacillus dendaii sp. nov. has been proposed. The type strain is skT53T (= NBRC 114101 T = TBRC 11241 T).

scholarly journals Rhodobium gokarnense sp. nov., a novel phototrophic alphaproteobacterium from a saltern

2007 ◽  
Vol 57 (5) ◽  
pp. 932-935 ◽  
Author(s):  
T. N. R. Srinivas ◽  
P. Anil Kumar ◽  
Ch. Sasikala ◽  
Ch. V. Ramana ◽  
J. F. Imhoff
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Hybridization Data

A pink-pigmented, phototrophic, purple nonsulfur bacterium, strain JA173T, was isolated in pure culture from a saltern in Gokarna, India, in a medium containing 2 % (w/v) NaCl. Strain JA173T was a non-motile Gram-negative rod that multiplied by budding. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain JA173T clusters with the class Alphaproteobacteria; highest sequence similarity (98 %) was to the type strain of Rhodobium orientis and 94 % similarity was observed to the 16S rRNA gene sequence of the type strain of Rhodobium marinum. However, DNA–DNA hybridization with R. orientis DSM 11290T revealed a relatedness value of only 35.1 % with strain JA173T. Strain JA173T contained lamellar internal membranes, bacteriochlorophyll a and carotenoids of the spirilloxanthin series. Strain JA173T had an obligate requirement for NaCl (optimum growth at 2–6 %, w/v) and grew photoheterotrophically with a number of organic compounds as carbon source or electron donor. Photoautotrophic, chemoautotrophic and fermentative growth could not be demonstrated. Yeast extract was required for growth. Based on 16S rRNA gene sequence analysis, DNA–DNA hybridization data and morphological and physiological characteristics, strain JA173T is sufficiently different from other species of the genus Rhodobium to be recognized as a representative of a novel species, Rhodobium gokarnense sp. nov. The type strain is JA173T (=ATCC BAA-1215T=DSM 17935T=JCM 13532T).

scholarly journals Exiguobacterium aestuarii sp. nov. and Exiguobacterium marinum sp. nov., isolated from a tidal flat of the Yellow Sea in Korea

2005 ◽  
Vol 55 (2) ◽  
pp. 885-889 ◽  
Author(s):  
In-Gi Kim ◽  
Mi-Hwa Lee ◽  
Seo-Youn Jung ◽  
Jae Jun Song ◽  
Tae-Kwang Oh ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Yellow Sea ◽  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence

Three Gram-variable, rod-shaped bacterial strains, TF-16T, TF-19 and TF-80T, were isolated from a tidal flat of Daepo Beach (Yellow Sea) near Mokpo City, Korea, and their taxonomic positions were investigated by a polyphasic approach. These isolates grew optimally in the presence of 2 % NaCl and at 30 °C. Their peptidoglycan types were based on l-Lys–Gly. The predominant menaquinone detected in the three strains was MK-7. The three strains contained large amounts of the branched fatty acids iso-C17 : 0, anteiso-C13 : 0, iso-C13 : 0 and iso-C15 : 0. The DNA G+C contents of strains TF-16T, TF-19 and TF-80T were 48·6, 48·4 and 48·0 mol%, respectively. The three strains formed a coherent cluster with Exiguobacterium species in a phylogenetic tree based on 16S rRNA gene sequences. They showed closest phylogenetic affiliation to Exiguobacterium aurantiacum, with 16S rRNA gene sequence similarity values of 98·1–98·3 %. The three strains exhibited 16S rRNA gene sequence similarity values of 94·0–94·6 % to the type strains of other Exiguobacterium species. Levels of DNA–DNA relatedness indicated that strains TF-16T and TF-19 and strain TF-80T are members of two species that are separate from E. aurantiacum. On the basis of phenotypic, phylogenetic and genetic data, strains TF-16T and TF-19 and strain TF-80T represent two novel species in the genus Exiguobacterium; the names Exiguobacterium aestuarii sp. nov. (type strain TF-16T=KCTC 19035T=DSM 16306T; reference strain TF-19) and Exiguobacterium marinum sp. nov. (type strain TF-80T=KCTC 19036T=DSM 16307T) are proposed.

scholarly journals Bacillus thermolactis sp. nov., isolated from dairy farms, and emended description of Bacillus thermoamylovorans

2011 ◽  
Vol 61 (8) ◽  
pp. 1954-1961 ◽  
Author(s):  
An Coorevits ◽  
Niall A. Logan ◽  
Anna E. Dinsdale ◽  
Gillian Halket ◽  
Patsy Scheldeman ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Emended Description

A polyphasic taxonomic study was performed on 22 thermotolerant, aerobic, endospore-forming bacteria from dairy environments. Seventeen isolates were retrieved from raw milk, one from a filter cloth and four from grass, straw or milking equipment. These latter four isolates (R-6546, R-7499, R-7764 and R-7440) were identified as Bacillus thermoamylovorans based on DNA–DNA hybridizations (values above 70 % with Bacillus thermoamylovorans LMG 18084T) but showed discrepancies in characteristics with the original species description, so an emended description of this species is given. According to 16S rRNA gene sequence analysis and DNA–DNA hybridization experiments, the remaining 18 isolates (R-6488T, R-28193, R-6491, R-6492, R-7336, R-33367, R-6486, R-6770, R-31288, R-28160, R-26358, R-7632, R-26955, R-26950, R-33520, R-6484, R-26954 and R-7165) represented one single species, most closely related to Bacillus thermoamylovorans (93.9 % 16S rRNA gene sequence similarity), for which the name Bacillus thermolactis is proposed. Cells were Gram-stain-positive, facultatively anaerobic, endospore-forming rods that grew optimally at 40–50 °C. The cell wall peptidoglycan type of strain R-6488T, the proposed type strain, was A1γ based on meso-diaminopimelic acid. Major fatty acids of the strains were C16 : 0 (28.0 %), iso-C16 : 0 (12.1 %) and iso-C15 : 0 (12.0 %). MK-7 was the predominant menaquinone, and major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and some unidentified phospholipids. DNA G+C content was 35.0 mol%. Phenotypic properties allowed discrimination from other thermotolerant species of the genus Bacillus and supported the description of the novel species Bacillus thermolactis, with strain R-6488T ( = LMG 25569T  = DSM 23332T) as the proposed type strain.

scholarly journals Lysobacter novalis sp. nov., isolated from fallow farmland soil

2015 ◽  
Vol 65 (Pt_9) ◽  
pp. 3131-3136 ◽  
Author(s):  
Hina Singh ◽  
Juan Du ◽  
Kyung-Hwa Won ◽  
Jung-Eun Yang ◽  
Shahina Akter ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Gliding Motility ◽  
Rrna Gene ◽  
The Novel ◽  
Respiratory Quinone ◽  
Gene Sequence Analysis ◽  
Farmland Soil ◽  
Major Respiratory Quinone

A novel bacterial strain, designated THG-PC7T, was isolated from fallow farmland soil in Yongin, South Korea. Cells of strain THG-PC7T were Gram-stain-negative, dark yellow, aerobic, rod-shaped and had gliding motility. Strain THG-PC7T grew optimally at 25–35 °C, at pH 7 and in the absence of NaCl. Comparative 16S rRNA gene sequence analysis identified strain THG-PC7T as belonging to the genus Lysobacter, exhibiting highest sequence similarity with Lysobacter ximonensis KCTC 22336T (98.7 %) followed by Lysobacter niastensis KACC 11588T (95.7 %). In DNA–DNA hybridization tests, DNA relatedness between strain THG-PC7T and its closest phylogenetic neighbour L. ximonensis was below 25 %. The DNA G+C content of the novel isolate was determined to be 62.5 mol%. Flexirubin-type pigments were found to be present. The major cellular fatty acids were determined to be iso-C15 : 0, iso-C16 : 0, anteiso-C15 : 0 and iso-C17 : 1ω9c. The major respiratory quinone was identified as ubiquonone-8 (Q8). The predominant polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and an unidentified aminophospolipid. On the basis of results from DNA–DNA hybridization and the polyphasic data, strain THG-PC7T represents a novel species of the genus Lysobacter, for which the name Lysobacter novalis sp. nov. is proposed. The type strain is THG-PC7T( = KACC 18276T = CCTCC AB 2014319T).

scholarly journals Rarimicrobium hominis gen. nov., sp. nov., representing the fifth genus in the phylum Synergistetes that includes human clinical isolates

2015 ◽  
Vol 65 (Pt_11) ◽  
pp. 3965-3970 ◽  
Author(s):  
Estelle Jumas-Bilak ◽  
Philippe Bouvet ◽  
Emma Allen-Vercoe ◽  
Fabien Aujoulat ◽  
Paul A. Lawson ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Clinical Isolates ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Rrna Gene Sequence

Five human clinical isolates of an unknown, strictly anaerobic, slow-growing, Gram-stain-negative, rod-shaped micro-organism were subjected to a polyphasic taxonomic study. Comparative 16S rRNA gene sequence-based phylogeny showed that the isolates grouped in a clade that included members of the genera Pyramidobacter, Jonquetella, and Dethiosulfovibrio; the type strain of Pyramidobacter piscolens was the closest relative with 91.5–91.7 % 16S rRNA gene sequence similarity. The novel strains were mainly asaccharolytic and unreactive in most conventional biochemical tests. Major metabolic end products in trypticase/glucose/yeast extract broth were acetic acid and propionic acid and the major cellular fatty acids were C13 : 0 and C16 : 0, each of which could be used to differentiate the strains from P. piscolens. The DNA G+C content based on whole genome sequencing for the reference strain 22-5-S 12D6FAA was 57 mol%. Based on these data, a new genus, Rarimicrobium gen. nov., is proposed with one novel species, Rarimicrobium hominis sp. nov., named after the exclusive and rare finding of the taxon in human samples. Rarimicrobium is the fifth genus of the 14 currently characterized in the phylum Synergistetes and the third one in subdivision B that includes human isolates. The type strain of Rarimicrobium hominis is ADV70T ( = LMG 28163T = CCUG 65426T).

scholarly journals Spirosoma telluris sp. nov. and Spirosoma arboris sp. nov. isolated from soil and tree bark, respectively

2020 ◽  
Vol 70 (10) ◽  
pp. 5355-5362 ◽  
Author(s):  
Heeyoung Kang ◽  
Inseong Cha ◽  
Haneul Kim ◽  
Kiseong Joh
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
Sequence Similarity ◽  
Polar Lipids ◽  
Tree Bark ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type

Two novel strains (HMF3257T and HMF4905T), isolated from freshwater and bark samples, were investigated to determine their relationships within and between species of the genus Spirosoma by using a polyphasic approach. They were aerobic, Gram-stain-negative, non-motile and rod-shaped bacteria. The major fatty acids (>10%) in both strains were identified as summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) and C16 : 1 ω5c, while strains HMF3257T and HMF4905T contained a moderately high amount of C16 : 0 and iso-C15 : 0, respectively. The predominant respiratory quinone was MK-7 for both strains. In addition to phosphatidylethanolamine and one unidentified glycolipid, the polar lipid profile of strain HMF3257T consisted of three unidentified aminophospholipids, one unidentified aminolipid and two unidentified polar lipids, and that of strain HMF4905T consisted of one unidentified aminophospholipid, two unidentified aminolipids and three unidentified polar lipids. The DNA G+C contents of strains HMF3257T and HMF4905T were 47.2 and 46.4 mol%, respectively. Phylogenetic analysis based on 16S rRNA gene sequences showed that strains HMF3257T and HMF4905T are closely related to Spirosoma migulaei 15J9-8T (97.0 % sequence similarity), while sharing 97.4 % sequence similarity with each other. The average nucleotide identity value between strains HMF3257T and HMF4905T was 81.1 %, and the digital DNA–DNA hybridization value between these two strains was 24.4 %. Based on the above data, strains HMF3257T and HMF4905T represent two novel members within the genus Spirosoma , for which the names Spirosoma telluris sp. nov. and Spirosoma arboris sp. nov. are proposed, respectively. The type strain of S. telluris is HMF3257T (=KCTC 62463T=NBRC 112670T) and type strain of S. arboris is HMF4905T (=KCTC 72779T=NBRC 114270T).

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